Hdmf

Bug fixes
- Fixed an issue with `ExternalResources` where retrieving an object resources wasn't in the proper format for a Pandas DataFrame. Additionally, a boolean parameter for creating an object when checking the existence of an object was added. mavaylon1 [790](https://github.com/hdmf-dev/hdmf/pull/790)
- Fixed an issue with the `tox` tool when upgrading to tox 4. rly [802](https://github.com/hdmf-dev/hdmf/pull/802)
- Fixed export of newly added links to existing elements of the exported file. rly [808](https://github.com/hdmf-dev/hdmf/pull/808)
- Added ``HDMFIO.__del__`` to ensure that I/O objects are being closed on delete. oruebel[811](https://github.com/hdmf-dev/hdmf/pull/811)

Minor improvements
- Added support for reading and writing `ExternalResources` to and from denormalized TSV files. mavaylon1 [799](https://github.com/hdmf-dev/hdmf/pull/799)
- Changed the name of `ExternalResources.export_to_sqlite` to `ExternalResources.to_sqlite`. mavaylon1 [799](https://github.com/hdmf-dev/hdmf/pull/799)
- Updated the tutorial for `ExternalResources`. mavaylon1 [799](https://github.com/hdmf-dev/hdmf/pull/799)
- Added `message` argument for assert methods defined by `hdmf.testing.TestCase` to allow developers to include custom error messages with asserts. oruebel [812](https://github.com/hdmf-dev/hdmf/pull/812)
- Clarify the expected chunk shape behavior for `DataChunkIterator`. oruebel [813](https://github.com/hdmf-dev/hdmf/pull/813)

Minor improvements
- Update CI, versioneer, and some requirements. rly ([786](https://github.com/hdmf-dev/hdmf/pull/786))

Bug fixes
- Fix an issue where not providing an optional argument to `__init__` of an auto-generated `MultiContainerInterface`
class raised an error. rly ([779](https://github.com/hdmf-dev/hdmf/pull/779))
- Fixed an issue with the `data_utils.GenericDataChunkIterator` where if the underlying dataset was such that the `numpy.product` of the `maxshape` exceeded the range of the default `int32`, buffer overflow would occur and cause the true buffer shape to exceed available memory. This has been resolved by dropping all `numpy` operations (which forced casting within the passed data type) in favor of the unlimited precision of Python builtin integer types codycbakerphd ([780](https://github.com/hdmf-dev/hdmf/pull/780)) ([#781](https://github.com/hdmf-dev/hdmf/pull/781))

Minor improvements
- When data is not specified in DataIO, 1) require dtype and shape both be specified and 2) determine length from shape. ajtritt ([771](https://github.com/hdmf-dev/hdmf/pull/771))

Bug fixes
- Fix an issue when autogenerating a class that extends a class where the constructor docval does not include all of
the fields (i.e., when the constructor sets some fields to fixed values). rly
([773](https://github.com/hdmf-dev/hdmf/pull/773))

Minor improvements
- Allow passing arguments through to column class constructor (argument `col_cls`) when calling `DynamicTable.add_column`. ajtritt ([769](https://github.com/hdmf-dev/hdmf/pull/769))

Bug fixes
- Fixed missing dependency "packaging" introduced in 3.4.3. The code has been updated to avoid the dependency. rly oruebel ([770](https://github.com/hdmf-dev/hdmf/pull/770))

Minor improvements
- Began to deprecate the use of the testing script `test.py` in favor of `pytest` and `test_gallery.py`.
rly ([760](https://github.com/hdmf-dev/hdmf/pull/760))
- Updated installation and maintainer documentation. rly ([760](https://github.com/hdmf-dev/hdmf/pull/760))

Bug fixes
- Fixed CI and flake8 issues. rly ([760](https://github.com/hdmf-dev/hdmf/pull/760))
- Updated uses of pandas.DataFrame.set_index to avoid FutureWarnings for pandas >=1.5.x oruebel ([762](https://github.com/hdmf-dev/hdmf/pull/762))
- Fixed broken `hdmf.common.get_hdf5io` function. rly ([765](https://github.com/hdmf-dev/hdmf/pull/765))